Manganese in PDB 5xsp: The Catalytic Domain of Gdpp with 5'-Papa

The structure of The Catalytic Domain of Gdpp with 5'-Papa, PDB code: 5xsp was solved by F.Wang, L.Gu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.13 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.619, 117.263, 127.368, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.3

The binding sites of Manganese atom in the The Catalytic Domain of Gdpp with 5'-Papa (pdb code 5xsp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Catalytic Domain of Gdpp with 5'-Papa, PDB code: 5xsp:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Catalytic Domain of Gdpp with 5'-Papa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Catalytic Domain of Gdpp with 5'-Papa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:34.1 occ:1.00 OD2 A:ASP349 2.3 25.4 1.0 OD2 A:ASP497 2.3 28.3 1.0 OD1 A:ASP418 2.4 27.2 1.0 O A:HOH821 2.4 29.2 1.0 NE2 A:HIS442 2.5 29.6 1.0 OD2 A:ASP418 3.0 29.1 1.0 CG A:ASP418 3.0 27.4 1.0 O A:HOH966 3.1 25.1 1.0 CG A:ASP349 3.2 24.5 1.0 CG A:ASP497 3.3 28.2 1.0 CD2 A:HIS442 3.5 30.5 1.0 CE1 A:HIS442 3.5 29.4 1.0 CB A:ASP349 3.5 25.9 1.0 MN A:MN702 3.5 62.7 1.0 OD1 A:ASP497 3.6 26.7 1.0 N A:THR465 4.3 20.6 1.0 OG1 A:THR465 4.4 24.4 1.0 OD1 A:ASP349 4.4 22.5 1.0 CE1 A:HIS443 4.4 47.8 1.0 CB A:ASP418 4.5 25.6 1.0 CA A:SER464 4.5 25.7 1.0 NE2 A:HIS443 4.5 46.4 1.0 ND1 A:HIS442 4.6 31.1 1.0 CG A:HIS442 4.6 31.1 1.0 CB A:ASP497 4.6 28.0 1.0 CB A:SER464 4.8 23.0 1.0 C A:SER464 4.9 25.5 1.0 CA A:ASP349 4.9 21.9 1.0

Manganese binding site 2 out of 4 in the The Catalytic Domain of Gdpp with 5'-Papa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Catalytic Domain of Gdpp with 5'-Papa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:62.7 occ:1.00 OD2 A:ASP418 2.4 29.1 1.0 O A:HOH821 2.4 29.2 1.0 OD2 A:ASP347 2.5 34.0 1.0 NE2 A:HIS343 2.6 34.8 1.0 OD1 A:ASP347 2.9 32.1 1.0 CG A:ASP347 3.1 30.6 1.0 CD2 A:HIS343 3.4 37.0 1.0 CG A:ASP418 3.5 27.4 1.0 MN A:MN701 3.5 34.1 1.0 CE1 A:HIS343 3.5 31.5 1.0 O A:HOH966 3.9 25.1 1.0 OD1 A:ASP418 4.0 27.2 1.0 O A:ASP418 4.5 25.7 1.0 CB A:ASP347 4.5 24.2 1.0 CG A:HIS343 4.5 32.3 1.0 ND1 A:HIS343 4.6 33.9 1.0 CB A:ASP418 4.6 25.6 1.0 CB A:ASP349 4.7 25.9 1.0 N A:ALA350 4.7 22.0 1.0 CB A:ALA350 4.8 23.4 1.0 OD1 A:ASP497 4.9 26.7 1.0 O A:HOH904 4.9 30.0 1.0 OD2 A:ASP349 5.0 25.4 1.0

Manganese binding site 3 out of 4 in the The Catalytic Domain of Gdpp with 5'-Papa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Catalytic Domain of Gdpp with 5'-Papa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:33.6 occ:1.00 O B:HOH845 1.9 30.6 1.0 OD2 B:ASP349 2.3 24.5 1.0 OD2 B:ASP497 2.4 30.0 1.0 OD1 B:ASP418 2.4 26.5 1.0 NE2 B:HIS442 2.6 29.8 1.0 OD2 B:ASP418 2.8 23.9 1.0 CG B:ASP418 2.9 25.8 1.0 CG B:ASP349 3.3 26.5 1.0 O B:HOH912 3.4 46.4 1.0 CG B:ASP497 3.4 30.9 1.0 CD2 B:HIS442 3.4 25.8 1.0 MN B:MN702 3.5 62.8 1.0 CE1 B:HIS442 3.6 31.1 1.0 CB B:ASP349 3.6 23.2 1.0 OD1 B:ASP497 3.8 29.9 1.0 CE1 B:HIS443 4.3 41.6 1.0 NE2 B:HIS443 4.3 51.4 1.0 N B:THR465 4.3 25.8 1.0 OG1 B:THR465 4.4 23.9 1.0 CB B:ASP418 4.4 21.5 1.0 OD1 B:ASP349 4.4 24.7 1.0 CA B:SER464 4.4 24.7 1.0 CG B:HIS442 4.6 30.9 1.0 ND1 B:HIS442 4.6 29.3 1.0 CB B:SER464 4.7 26.8 1.0 CB B:ASP497 4.7 25.7 1.0 C B:SER464 4.9 27.7 1.0

Manganese binding site 4 out of 4 in the The Catalytic Domain of Gdpp with 5'-Papa


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Catalytic Domain of Gdpp with 5'-Papa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn702 b:62.8 occ:1.00 O B:HOH845 2.2 30.6 1.0 OD2 B:ASP418 2.5 23.9 1.0 OD2 B:ASP347 2.5 38.2 1.0 NE2 B:HIS343 2.6 31.2 1.0 OD1 B:ASP347 3.0 32.5 1.0 CG B:ASP347 3.1 28.0 1.0 CD2 B:HIS343 3.4 29.6 1.0 CE1 B:HIS343 3.5 35.8 1.0 MN B:MN701 3.5 33.6 1.0 CG B:ASP418 3.5 25.8 1.0 O B:HOH912 3.9 46.4 1.0 OD1 B:ASP418 4.1 26.5 1.0 O B:ASP418 4.5 25.3 1.0 CG B:HIS343 4.5 35.2 1.0 ND1 B:HIS343 4.5 37.8 1.0 CB B:ASP347 4.6 29.6 1.0 CB B:ASP418 4.7 21.5 1.0 OD1 B:ASP497 4.8 29.9 1.0 CB B:ALA350 4.8 26.1 1.0 N B:ALA350 4.8 25.7 1.0 CB B:ASP349 4.8 23.2 1.0 OD2 B:ASP497 4.9 30.0 1.0 OD2 B:ASP349 5.0 24.5 1.0

F.Wang, Q.He, K.Su, T.Wei, S.Xu, L.Gu. Structural and Biochemical Characterization of the Catalytic Domains of Gdpp Reveals A Unified Hydrolysis Mechanism For the Dhh/DHHA1 Phosphodiesterase Biochem. J. V. 475 191 2018.
ISSN: ESSN 1470-8728
PubMed: 29203646
DOI: 10.1042/BCJ20170739